35378 add metagenomic support (#19)

* Added metagenomics_batch_api.py and metagenomics_batch_item_api.py

* Added MetagenomicsBatch.py and MetagenomicsBatchItem.py

* Added schema.py files for Metagenomics support

* Class name correction

* Corrections in Schema and Entity files

* Added schema tests

* Minor correction

* Schema tests pass

* Added create test for Metagenomics Batch and Batch Items

* - Removed writing to file for metagenomic batch test,

---------

Co-authored-by: John Phan <[email protected]>

dinapy/apis/seqdbapi/metagenomics_batch_api.py

@@ -0,0 +1,33 @@
+"""Class that extracts common functionality for Metagenomics Batch entity"""  
+
+from .seqdbapi import SeqDBApi	
+
+class MetagenomicsBatchApi(SeqDBApi):
+
+  def __init__(self, config_path: str = None, base_url: str = None) -> None:
+    """
+    Parameters:
+        config_path (str, optional): Path to a config file (default: None).
+        base_url (str, optional): URL to the URL to perform the API requests against. If not
+        provided then local deployment URL is used. Should end with a forward slash.
+    """
+    super().__init__(config_path, base_url)
+    self.base_url += "metagenomics-batch"
+
+  def get_relationship_entity(self, entity_id, endpoint):
+    entity_id = str(entity_id) if isinstance(entity_id, int) else entity_id
+    new_request_url = self.base_url + '/'+ str(entity_id) + f'/relationships/{endpoint}'
+    print(new_request_url)
+    jsn_resp = self.get_req_dina(request_url = new_request_url)
+    return jsn_resp if jsn_resp else ''   
+
+  def get_entity_with_param(self, entity_id,param):
+    entity_id = str(entity_id) if isinstance(entity_id, int) else entity_id
+    new_request_url = self.base_url + '/' + entity_id
+    jsn_resp = self.get_req_dina(new_request_url, params = param)
+    return jsn_resp if jsn_resp else '' 
+
+  def get_entity_by_param(self, param=None):
+    print(self.base_url,param)
+    jsn_resp = self.get_req_dina(self.base_url, params = param)
+    return jsn_resp if jsn_resp else ''

dinapy/apis/seqdbapi/metagenomics_batch_item_api.py

@@ -0,0 +1,33 @@
+"""Class that extracts common functionality for Metagenomics Batch Item entity"""  
+
+from .seqdbapi import SeqDBApi	
+
+class MetagenomicsBatchItemApi(SeqDBApi):
+
+  def __init__(self, config_path: str = None, base_url: str = None) -> None:
+    """
+    Parameters:
+        config_path (str, optional): Path to a config file (default: None).
+        base_url (str, optional): URL to the URL to perform the API requests against. If not
+        provided then local deployment URL is used. Should end with a forward slash.
+    """
+    super().__init__(config_path, base_url)
+    self.base_url += "metagenomics-batch-item"
+
+  def get_relationship_entity(self, entity_id, endpoint):
+    entity_id = str(entity_id) if isinstance(entity_id, int) else entity_id
+    new_request_url = self.base_url + '/'+ str(entity_id) + f'/relationships/{endpoint}'
+    print(new_request_url)
+    jsn_resp = self.get_req_dina(request_url = new_request_url)
+    return jsn_resp if jsn_resp else ''   
+
+  def get_entity_with_param(self, entity_id,param):
+    entity_id = str(entity_id) if isinstance(entity_id, int) else entity_id
+    new_request_url = self.base_url + '/' + entity_id
+    jsn_resp = self.get_req_dina(new_request_url, params = param)
+    return jsn_resp if jsn_resp else '' 
+
+  def get_entity_by_param(self, param=None):
+    print(self.base_url,param)
+    jsn_resp = self.get_req_dina(self.base_url, params = param)
+    return jsn_resp if jsn_resp else ''

dinapy/entities/MetagenomicsBatch.py

@@ -0,0 +1,76 @@
+class MetagenomicsBatchDTO:
+    def __init__(self, id=None, type=None, attributes=None, relationships=None):
+        self.id = id
+        self.type = type
+        self.attributes = attributes
+        self.relationships = relationships
+
+    def get_id(self):
+        return self.id
+
+    def get_type(self):
+        return self.type
+
+class MetagenomicsBatchDTOBuilder:
+    def __init__(self):
+        self._id = None
+        self._type = 'metagenomics-batch'
+        self._attributes = None
+        self._relationships = None
+
+    def set_id(self, id):
+        self._id = id
+        return self
+
+    def set_type(self, type):
+        self._type = type
+        return self
+
+    def set_attributes(self, attributes):
+        self._attributes = attributes
+        return self
+
+    def set_relationships(self, relationships):
+        self._relationships = relationships
+        return self
+
+    def build(self):
+        return MetagenomicsBatchDTO(self._id, self._type, self._attributes, self._relationships)
+
+class MetagenomicsBatchAttributesDTO:
+    def __init__(self, createdBy=None, createdOn=None, group=None, name=None):
+        self.createdBy = createdBy
+        self.createdOn = createdOn
+        self.group = group
+        self.name = name
+
+class MetagenomicsBatchAttributesDTOBuilder:
+    def __init__(self):
+        self._createdBy = 'undefined'
+        self._createdOn = 'undefined'
+        self._group = 'undefined'
+        self._name = 'undefined'
+
+    def set_createdBy(self, createdBy):
+        self._createdBy = createdBy
+        return self
+
+    def set_createdOn(self, createdOn):
+        self._createdOn = createdOn
+        return self
+
+    def set_group(self, group):
+        self._group = group
+        return self
+
+    def set_name(self, name):
+        self._name = name
+        return self
+
+    def build(self):
+        return MetagenomicsBatchAttributesDTO(
+            self._createdBy, 
+            self._createdOn, 
+            self._group, 
+            self._name
+        )

dinapy/entities/MetagenomicsBatchItem.py

@@ -0,0 +1,62 @@
+class MetagenomicsBatchItemDTO:
+    def __init__(self, id=None, type=None, attributes=None, relationships=None):
+        self.id = id
+        self.type = type
+        self.attributes = attributes
+        self.relationships = relationships
+
+    def get_id(self):
+        return self.id
+
+    def get_type(self):
+        return self.type
+
+class MetagenomicsBatchItemDTOBuilder:
+    def __init__(self):
+        self._id = None
+        self._type = 'metagenomics-batch-item'
+        self._attributes = None
+        self._relationships = None
+
+    def set_id(self, id):
+        self._id = id
+        return self
+
+    def set_type(self, type):
+        self._type = type
+        return self
+
+    def set_attributes(self, attributes):
+        self._attributes = attributes
+        return self
+
+    def set_relationships(self, relationships):
+        self._relationships = relationships
+        return self
+
+    def build(self):
+        return MetagenomicsBatchItemDTO(self._id, self._type, self._attributes, self._relationships)
+
+class MetagenomicsBatchItemAttributesDTO:
+    def __init__(self, createdBy=None, createdOn=None):
+        self.createdBy = createdBy
+        self.createdOn = createdOn
+
+class MetagenomicsBatchItemAttributesDTOBuilder:
+    def __init__(self):
+        self._createdBy = 'undefined'
+        self._createdOn = 'undefined'
+
+    def set_createdBy(self, createdBy):
+        self._createdBy = createdBy
+        return self
+
+    def set_createdOn(self, createdOn):
+        self._createdOn = createdOn
+        return self
+
+    def build(self):
+        return MetagenomicsBatchItemAttributesDTO(
+            self._createdBy, 
+            self._createdOn
+        )

dinapy/schemas/metagenomics_batch_item_schema.py

@@ -0,0 +1,58 @@
+# This file holds schemas for serializing and deserializing MetagenomicsBatchItem entities
+# using the JSON API format. It utilizes the marshmallow_jsonapi library.
+from marshmallow_jsonapi import Schema, fields
+from marshmallow import post_load,pre_load,post_dump,ValidationError
+
+from dinapy.entities.MetagenomicsBatchItem import MetagenomicsBatchItemDTO
+from .customFields import SkipUndefinedField
+from .BaseSchema import *
+
+class MetagenomicsBatchSchema(BaseSchema):
+    class Meta:
+        type_ = 'metagenomics-batch'
+
+class PcrBatchItemSchema(BaseSchema):
+    class Meta:
+        type_ = 'pcr-batch-item'
+
+class MolecularAnalysisRunItemSchema(BaseSchema):
+    class Meta:
+        type_ = 'molecular-analysis-run-item'
+
+class NgsIndexSchema(BaseSchema):
+    class Meta:
+        type_ = 'ngs-index'
+
+class MetagenomicsBatchItemSchema(Schema):
+    id = fields.Str(load_only=True)
+    createdBy = SkipUndefinedField(fields.Str, attribute="attributes.createdBy")
+    createdOn = SkipUndefinedField(fields.Str, load_only=True, attribute="attributes.createdOn")
+
+    metagenomicsBatch = create_relationship("metagenomics-batch-item", "metagenomics-batch", "metagenomicsBatch")
+    pcrBatchItem = create_relationship("metagenomics-batch-item", "pcr-batch-item", "pcrBatchItem")
+    molecularAnalysisRunItem = create_relationship("metagenomics-batch-item", "molecular-analysis-run-item", "molecularAnalysisRunItem")
+    indexI5 = create_relationship("metagenomics-batch-item", "ngs-idnex", "indexI5")
+    indexI7 = create_relationship("metagenomics-batch-item", "ngs-idnex", "indexI7")
+
+    @post_load
+    def set_none_to_undefined(self, data, **kwargs):
+        for attr in data.attributes:
+            if data.attributes[attr] is None:
+                data.attributes[attr] = 'undefined'
+        return data
+
+    @post_dump
+    def remove_skipped_fields(self, data, many, **kwargs):
+        # Remove fields with the special marker value
+        return {key: value for key, value in data.items() if value is not SkipUndefinedField(fields.Field).SKIP_MARKER}
+
+    @post_load
+    def object_deserialization(self, data, **kwargs):
+        if 'meta' in data:
+            del data['meta']
+        return MetagenomicsBatchItemDTO(**data)
+
+    meta = fields.DocumentMeta()
+
+    class Meta:
+        type_ = 'metagenomics-batch-item'

dinapy/schemas/metagenomics_batch_schema.py

@@ -0,0 +1,49 @@
+# This file holds schemas for serializing and deserializing MetagenomicsBatch entities
+# using the JSON API format. It utilizes the marshmallow_jsonapi library.
+from marshmallow_jsonapi import Schema, fields
+from marshmallow import post_load,pre_load,post_dump,ValidationError
+
+from dinapy.entities.MetagenomicsBatch import MetagenomicsBatchDTO
+from .customFields import SkipUndefinedField
+from .BaseSchema import *
+
+class ProtocolSchema(BaseSchema):
+    class Meta:
+        type_ = 'protocol'
+
+class IndexSetSchema(BaseSchema):
+    class Meta:
+        type_ = 'index-set'
+
+class MetagenomicsBatchSchema(Schema):
+    id = fields.Str(load_only=True)
+    createdBy = SkipUndefinedField(fields.Str, load_only=True, attribute="attributes.createdBy")
+    createdOn = SkipUndefinedField(fields.Str, load_only=True, attribute="attributes.createdOn")
+    group = SkipUndefinedField(fields.Str, required=True, attribute="attributes.group")
+    name = SkipUndefinedField(fields.Str, attribute="attributes.name")
+
+    protocol = create_relationship("metagenomics-batch", "protocol")
+    indexSet = create_relationship("metagenomics-batch", "index-set", "indexSet")
+
+    @post_load
+    def set_none_to_undefined(self, data, **kwargs):
+        for attr in data.attributes:
+            if data.attributes[attr] is None:
+                data.attributes[attr] = 'undefined'
+        return data
+
+    @post_dump
+    def remove_skipped_fields(self, data, many, **kwargs):
+        # Remove fields with the special marker value
+        return {key: value for key, value in data.items() if value is not SkipUndefinedField(fields.Field).SKIP_MARKER}
+
+    @post_load
+    def object_deserialization(self, data, **kwargs):
+        if 'meta' in data:
+            del data['meta']
+        return MetagenomicsBatchDTO(**data)
+
+    meta = fields.DocumentMeta()
+
+    class Meta:
+        type_ = 'metagenomics-batch'